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Figure 2 from: Ebinghaus M, Maier W, Wingfield MJ, Begerow D (2018) New host associations and a novel species for the gall-inducing acacia rust genus Ravenelia in South Africa. MycoKeys 43: 1-21. https://doi.org/10.3897/mycokeys.43.25090
Figure 2 Biplots of a principal component analysis (PCA) of six teliospore characteristics of specimens of ARaveneliamacowaniana originating from Vachelliakarroo (red) and V.natalitia (green) and B in comparison with R.xanthophloeae sp. nov. collected from V.xanthophloea (blue) C, D represent R.evansii originating from seven distinct Vachellia species. Each dot represents an individual teliospore for which mean values of multiple measurements of all six defined morphological characteristics were calculated. Each colour represents the host species of the individual rust specimen. In D only spore representatives collected from V.borleae, V.exuvialis and V.davyi were highlighted to gain better visibility.
Figure 5 from: Chen W-H, Liu C, Han Y-F, Liang J-D, Tian W-Y, Liang Z-Q (2019) Three novel insect-associated species of Simplicillium (Cordycipitaceae, Hypocreales) from Southwest China. MycoKeys 58: 83-102. https://doi.org/10.3897/mycokeys.58.37176
Figure 5 Simplicillium formicidaeA isolated substrate an infected ant (Hymenoptera) B–C culture plate, showing the front (B) and the reverse (C) of the colony, cultured on PDA medium D, E phialides solitary, conidia adhering globose slimy head and conidia F conidia. Scale bars: 10 mm (B, C), 10μm (D, E, F).
Figure 4 from: Chen W-H, Liu C, Han Y-F, Liang J-D, Tian W-Y, Liang Z-Q (2019) Three novel insect-associated species of Simplicillium (Cordycipitaceae, Hypocreales) from Southwest China. MycoKeys 58: 83-102. https://doi.org/10.3897/mycokeys.58.37176
Figure 4 Simplicillium lepidopterorumA infected carpenterworm (Lepidoptera) B, C culture plate, showing the front (B) and the reverse (C) of the colony, cultured on PDA medium D, E, F phialides solitary and conidia in globose heads D conidia. Scale bars: 10 mm (B, C), 10μm (D, E, F, G).
Figure 3 from: Chen W-H, Liu C, Han Y-F, Liang J-D, Tian W-Y, Liang Z-Q (2019) Three novel insect-associated species of Simplicillium (Cordycipitaceae, Hypocreales) from Southwest China. MycoKeys 58: 83-102. https://doi.org/10.3897/mycokeys.58.37176
Figure 3 Simplicillium cicadellidaeA infected leafhopper (Hemiptera) B–C culture plate, showing the front (B) and the reverse (C) of the colony, cultured on PDA medium D–F phialides solitary, conidia adhering ellipsoidal slimy head and conidia G conidia. Scale bars: 10 mm (B, C), 10μm (D, E, F, G).
Figure 1 from: Chen W-H, Liu C, Han Y-F, Liang J-D, Tian W-Y, Liang Z-Q (2019) Three novel insect-associated species of Simplicillium (Cordycipitaceae, Hypocreales) from Southwest China. MycoKeys 58: 83-102. https://doi.org/10.3897/mycokeys.58.37176
Figure 1 Phylogenetic relationships among the genus Simplicillium and its allies in Cordycipitaceae based on multigene dataset (LSU, RPB1, RPB2 and TEF). Statistical support values (≥ 0.5/50%) are shown at the nodes for ML bootstrap support/BI posterior probabilities. The tree is rooted with Purpureocillium lilacinum (CBS 284.36 and CBS 431.87). The new species are in bold face. T in the upper right corner indicates the type strains.
Figure 2 from: Chen W-H, Liu C, Han Y-F, Liang J-D, Tian W-Y, Liang Z-Q (2019) Three novel insect-associated species of Simplicillium (Cordycipitaceae, Hypocreales) from Southwest China. MycoKeys 58: 83-102. https://doi.org/10.3897/mycokeys.58.37176
Figure 2 Phylogenetic relationships among the new taxa S. cicadellidae, S. formicidae, S. lepidopterorum and other Simplicillium species by ITS+LSU sequences. Statistical support values (≥ 0.5/50%) are shown at the nodes for ML bootstrap support/BI posterior probabilities. The tree is rooted with Pochonia chlamydosporia (CBS 103.65). The new species are in bold face. T in the upper right corner indicates the type strains.
FIGURES 5–7 Paracrias huberi 5 in Report of a novel biological association for Paracrias huberi Gumovsky (Hymenoptera: Eulophidae) with redescription of the female and description of the unknown male
FIGURES 5–7 Paracrias huberi 5. ♀ mesosoma, dorsal. 6. ♀ mesosoma, lateral. 7. ♂ mesosoma, dorsal.
Data from: Analysis of head and neck carcinoma progression reveals novel and relevant stage-specific changes associated with immortalisation and malignancy
Head and neck squamous cell carcinoma (HNSCC) is a widely prevalent cancer globally with high mortality and morbidity. We report here changes in the genomic landscape in the development of these tumours from potentially premalignant lesions (PPOLS) to malignancy and lymph node metastases. Frequent likely pathological mutations are restricted to a relatively small set of genes including TP53, CDKN2A, FBXW7, FAT1, NOTCH1 and KMT2D; these arise early in tumour progression and are present in PPOLs with NOTCH1 mutations restricted to cell lines from lesions that subsequently progressed to HNSCC. The most frequent genetic changes are of consistent somatic copy number alterations (SCNA). The earliest SCNAs involved deletions of CSMD1 (8p23.2), FHIT (3p14.2) and CDKN2A (9p21.3) together with gains of chromosome 20. CSMD1 deletions or promoter hypermethylation were present in all of the immortal PPOLs and occurred at high frequency in the immortal HNSCC cell lines (promoter hypermethylation ~63%, hemizygous deletions ~75%, homozygous deletions ~18%). Forced expression of CSMD1 in the HNSCC cell line H103 showed significant suppression of proliferation (p=0.0053) and invasion in vitro (p=5.98X10-5) supporting a role for CSMD1 inactivation in early head and neck carcinogenesis. In addition, knockdown of CSMD1 in the CSMD1-expressing BICR16 cell line showed significant stimulation of invasion in vitro (p=1.82 x 10-5) but not cell proliferation (p=0.239). HNSCC with and without nodal metastases showed some clear differences including high copy number gains of CCND1, hsa-miR-548k and TP63 in the metastases group. GISTIC peak SCNA regions showed significant enrichment (adj P<0.01) of genes in multiple KEGG cancer pathways at all stages with disruption of an increasing number of these involved in the progression to lymph node metastases. Sixty-seven genes from regions with statistically significant differences in SCNA/LOH frequency between immortal PPOL and HNSCC cell lines showed correlation with expression including 5 known cancer drivers.
Data from: Identification and validation of a novel immune-related signature associated with macrophages and CD8 T cell infiltration predicting overall survival for hepatocellular carcinoma
<p><b>Background:</b> Although the effects of macrophages and CD8 T cell infiltration on clinical outcomes have been widely reported, the association between immunity-associated gene with them for hepatocellular carcinoma (HCC) remains unclear.</p> <p><b>Materials and methods: </b>The ssGSEA served for quantifying the macrophages as well as CD8 T cell infiltration in the HCC samples obtained from TCGA database. Kaplan-Meier(KM) survival assay was used to determine the associations between macrophages and CD8 T cell infiltration with OS. LASSO Cox regressive method assisted in developing an immune gene signature as well as building a risk score. The performance was evaluated by the time-dependent ROC together with the KM survival analysis. The ICGC database were adopted for external verification. CIBERSORT was applied to the correlation analysis on the immune-related signature and the immunocyte infiltration. GSEA were employed exploring the underlying molecular mechanisms.</p> <p><b>Results:</b> Increased CD8+ T cell infiltration was associated with longer OS, whereas a greater infiltration of macrophages was related to shorter OS. There were 398 differential expression genes (DEGs) between the high- and low infiltration groups with the "edgeR" package. A prognostic signature consisted of 10 immune genes was built in TCGA and examined in ICGC. The uniform cutoff (0.927) was adopted for separating sufferers into the high-risk(HR) and low-risk(LR) groups. The ROC curves revealed that the AUC data for this signature predicting 1,2,3,4 and 5 year were all above 0.7 in both TCGA and ICGC cohort and patients in the HR<sub> </sub>group exhibited evidently weaker prognostic results compared with the LR group. The HR<sub> </sub>group presented evidently greater Tregs and Macrophage M0 relative to the LR group, whereas the LR group saw the enrichment of CD8 T cells.</p> <p><b>Conclusion:</b> The immune signature associated with macrophages as well as CD8 T cell infiltration has reliable prognostic and predictive value for HCC patients.</p>
Novel associations of BST1 and LAMP3 with rapid eye movement sleep behavior disorder: supplementary data
<p><b>Objective:</b> To examine the role of genes identified through genome-wide association studies (GWASs) of Parkinson disease (PD) in the risk of isolated rapid-eye-movement (REM) sleep behavior disorder (iRBD).</p> <p><b>Methods:</b> We fully sequenced 25 genes previously identified in GWASs of PD, in a total of 1,039 iRBD patients and 1,852 controls. The role of rare heterozygous variants in these genes was examined using burden tests. The contribution of biallelic variants was further tested. To examine the potential impact of rare nonsynonymous <i>BST1</i> variants on the protein structure, we performed <i>in silico</i> structural analysis. Finally, we examined the association of common variants using logistic regression adjusted for age and sex.</p> <p><b>Results:</b> We found an association between rare heterozygous nonsynonymous variants in <i>BST1</i> and iRBD (<i>p</i>=0.0003 at coverage >50X and 0.0004 at >30X), mainly driven by three nonsynonymous variants (p.V85M, p.I101V and p.V272M) found in 22 (1.2%) controls vs. two (0.2%) patients. All three variants seem to be loss-of-function variants with a potential effect on the protein structure and stability. Rare non-coding heterozygous variants in <i>LAMP3</i> were also associated with iRBD (<i>p</i>=0.0006 at >30X). We found no association between rare heterozygous variants in the rest of genes and iRBD. Several carriers of biallelic variants were identified, yet there was no overrepresentation in iRBD.</p> <p><b>Conclusion:</b> Our results suggest that rare coding variants in <i>BST1 </i>and rare non-coding variants in<i> LAMP3 </i>are associated with iRBD. Additional studies are required to replicate these results and examine whether loss-of-function of <i>BST1 </i>could be a therapeutic target.</p>
Figures 34-36 from: Zacharczenko B, Wagner D, Hatfield M (2014) A new cryptic Sympistis from eastern North America revealed by novel larval phenotype and host plant association (Lepidoptera, Noctuidae, Oncocnemidinae). ZooKeys 379: 93-107. https://doi.org/10.3897/zookeys.379.5765
Figures 34-36 - Sympistis forbesi IA: Boone Co., Little Blue Stem Prairie, May 2011 on Triosteum perfoliatum 34 three larvae secreted in a leaf axil; note frass accumulation 35 larvae on new spring leaves; note two larvae on new leaf bundle and one on foreground leaf 36 last instar on a flower of Triosteum perfoliatum, matching the color of the flower and petioles.
Figures 24-27 from: Zacharczenko B, Wagner D, Hatfield M (2014) A new cryptic Sympistis from eastern North America revealed by novel larval phenotype and host plant association (Lepidoptera, Noctuidae, Oncocnemidinae). ZooKeys 379: 93-107. https://doi.org/10.3897/zookeys.379.5765
Figures 24-27 - Sympistis forbesi middle instar. 24 head, lateral, with adenosma extruded; scale = 250 µm 25 labrum, mandibles, and oral cavity; scale = 100 µm 26 hypophryngeal complex (center left) and maxilla (center right); scale = 100 µm 27 prothoracic leg (note apical and subapical blade-like setae proximal to claws); scale = 100 µm.
Figures 13-18 from: Zacharczenko B, Wagner D, Hatfield M (2014) A new cryptic Sympistis from eastern North America revealed by novel larval phenotype and host plant association (Lepidoptera, Noctuidae, Oncocnemidinae). ZooKeys 379: 93-107. https://doi.org/10.3897/zookeys.379.5765
Figures 13-18 - Sympistis forbesi and Sympistis chionanthi genitalia 13 Sympistis forbesi HOLOTYPE male, IOWA: Boone Co., Little Blue Stem Prairie, Genitalia CNC slide # 16516 ♂; scale = 1 mm 14 aedoeagus, same data 15 Sympistis chionanthi male, MANITOBA, Cartwright, Genitalia CNC slide # 16515 ♂ 16 aedoeagus, same data 17 Sympistis chionanthi female, SASKATCHEWAN, 8 mi NW Stewart, 1800', Genitalia CNC slide # 13192 ♀; scale = 1 mm 18 Sympistis forbesi paratype female, same data as male, Genitalia CNC slide # 16517 ♀.
Figures 30-33 from: Zacharczenko B, Wagner D, Hatfield M (2014) A new cryptic Sympistis from eastern North America revealed by novel larval phenotype and host plant association (Lepidoptera, Noctuidae, Oncocnemidinae). ZooKeys 379: 93-107. https://doi.org/10.3897/zookeys.379.5765
Figures 30-33 - Sympistis forbesi and Sympistis chionanthi larvae. 30 Sympistis forbesi second (upper) and third (lower) instars. IA: Boone Co., Little Blue Stem Prairie, May 2011, ex Triosteum perfoliatum 31 Sympistis forbesi middle instar, same collection data 32 Sympistis forbesi mature last instar, same collection data 33 Sympistis chionanthi mature last instar, NY: Albany Co., Albany, female fall 1995, ex ova reared on Fraxinus americana, DLW Lot: 1996F32.
Figures 1-12 from: Zacharczenko B, Wagner D, Hatfield M (2014) A new cryptic Sympistis from eastern North America revealed by novel larval phenotype and host plant association (Lepidoptera, Noctuidae, Oncocnemidinae). ZooKeys 379: 93-107. https://doi.org/10.3897/zookeys.379.5765
Figures 1-12 - Adults of Sympistis forbesi and Sympistis chionanthi. 1 ♂ Sympistis forbesi HOLOTYPE, IA: Boone Co., Little Blue Stem Prairie, ex larva on Triosteum (UCMS) 2 ♂ Sympistis forbesi, IL: Champaign Co., Mahomet, ex larva on Triosteum (CUIC) 3 ♂ Sympistis chionanthi, NY: Tompkins Co., Ithaca, ex ova, reared on Fraxinus (CUIC) 4 ♂ Sympistis forbesi, IA: Boone Co., Little Blue Stem Prairie, ex larva on Triosteum (UCMS) 5 ♂ Sympistis forbesi, IL: Champaign Co., Mahomet, ex larva on Triosteum (CUIC) 6 ♂ Sympistis chionanthi, CT: Windham Co., Hampton, adult at light (UCMS) 7 ♀ Sympistis forbesi, IA: Boone Co., Little Blue Stem Prairie, ex larva on Triosteum (UCMS) 8 ♀ Sympistis forbesi, IL: Champaign Co., Mahomet, ex larva on Triosteum (CUIC) 9 ♀ Sympistis chionanthi, NY: Tompkins Co., Ithaca, ex ova, reared on Fraxinus (CUIC) 10 ♀ Sympistis forbesi, IA: Polk Co., ex larva on Triosteum (UCMS) 11 ♀ Sympistis forbesi, IL: Champaign Co., Mahomet, ex larva on Triosteum (CUIC) 12 ♀ Sympistis chionanthi, CT: Windham Co., Pomfret, adult at light (UCMS).
Figures 19-23 from: Zacharczenko B, Wagner D, Hatfield M (2014) A new cryptic Sympistis from eastern North America revealed by novel larval phenotype and host plant association (Lepidoptera, Noctuidae, Oncocnemidinae). ZooKeys 379: 93-107. https://doi.org/10.3897/zookeys.379.5765
Figures 19-23 - Sympistis forbesi larva. 19 chaetotaxy 20 head, lateral 21 head, frontal 22 labrum 23 mandible.
Figure 3 from: Morano E, Bonal R (2016) Cheiracanthium ilicis sp. n. (Araneae, Eutichuridae), a novel spider species associated with Holm Oaks (Quercus ilex). ZooKeys 601: 21-39. https://doi.org/10.3897/zookeys.601.8241
Figure 3 - DNA phylogeny of one mitochondrial (cox1) and one nuclear (28S) genes showing the phylogenetic position of Cheiracanthium ilicis sp. n. within its genus. Tree topology was inferred using maximum likelihood (GTR + I + Gamma substitution model) and Bayesian inference.
Figure 5 from: Morano E, Bonal R (2016) Cheiracanthium ilicis sp. n. (Araneae, Eutichuridae), a novel spider species associated with Holm Oaks (Quercus ilex). ZooKeys 601: 21-39. https://doi.org/10.3897/zookeys.601.8241
Figure 5 - Number of immatures (grey bars) and adults (black bars) Cheiracanthium ilicis sp. n. collected throughout the year.
Figure 1 from: Morano E, Bonal R (2016) Cheiracanthium ilicis sp. n. (Araneae, Eutichuridae), a novel spider species associated with Holm Oaks (Quercus ilex). ZooKeys 601: 21-39. https://doi.org/10.3897/zookeys.601.8241
Figure 1 - Palp of Cheiracanthium ilicis sp. n. In prolateral view (A), ventral (B) and retrolateral (C). Abbreviations: C (conductor); CS (cymbial spur); E (embolus); RTA (retrolateral tibial apophysis); TA (tegular apophysis).
Figure 4 from: Morano E, Bonal R (2016) Cheiracanthium ilicis sp. n. (Araneae, Eutichuridae), a novel spider species associated with Holm Oaks (Quercus ilex). ZooKeys 601: 21-39. https://doi.org/10.3897/zookeys.601.8241
Figure 4 - Relationship between the number of individuals collected and the tree size (canopy surface in m2).
ScienceDex guides
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These curated guides explain access requirements, typical timelines, costs, and reuse considerations for widely used research datasets.
Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
Annotated Behaviour and Observability Dataset (ABODe)
ABODe is a University of Edinburgh DataShare dataset for behavior classification in group-housed mice using home-cage video, identities, bounding boxes, ground-plate positions, and annotator labels.
DANDI Archive for NWB datasets
DANDI is a BRAIN Initiative archive for publishing and sharing neurophysiology data, including electrophysiology, optophysiology, and behavioral data packaged as NWB and related standards.
International Brain Laboratory public data
The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
OpenNeuro
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.